The comparative genomics and complex population history of Papio baboons

Jeffrey Rogers; Muthuswamy Raveendran; R. Alan Harris; Thomas Mailund; Kalle Leppälä; Georgios Athanasiadis; Mikkel Heide Schierup; Jade Cheng; Kasper Munch; Jerilyn A. Walker; Miriam K. Konkel; Vallmer Jordan; Cody J. Steely; Thomas O. Beckstrom; Christina Bergey; Andrew Burrell; Dominik Schrempf; Angela Noll; Maximillian Kothe; Gisela H. Kopp; Yue Liu; Shwetha Murali; Konstantinos Billis; Fergal J. Martin; Matthieu Muffato; Laura Cox; James Else; Todd Disotell; Donna M. Muzny; Jane Phillips-Conroy; Bronwen Aken; Evan E. Eichler; Tomas Marques-Bonet; Carolin Kosiol; Mark A. Batzer; Matthew W. Hahn; Jenny Tung; Dietmar Zinner; Christian Roos; Clifford J. Jolly; Richard A. Gibbs; Kim C. Worley; Baboon Genome Analysis Consortium

doi:10.1126/sciadv.aau6947

The comparative genomics and complex population history of Papio baboons

Jeffrey Rogers^*, Muthuswamy Raveendran, R. Alan Harris, Thomas Mailund, Kalle Leppälä, Georgios Athanasiadis, Mikkel Heide Schierup, Jade Cheng, Kasper Munch, Jerilyn A. Walker, Miriam K. Konkel, Vallmer Jordan, Cody J. Steely, Thomas O. Beckstrom, Christina Bergey, Andrew Burrell, Dominik Schrempf, Angela Noll, Maximillian Kothe, Gisela H. KoppYue Liu, Shwetha Murali, Konstantinos Billis, Fergal J. Martin, Matthieu Muffato, Laura Cox, James Else, Todd Disotell, Donna M. Muzny, Jane Phillips-Conroy, Bronwen Aken, Evan E. Eichler, Tomas Marques-Bonet, Carolin Kosiol, Mark A. Batzer, Matthew W. Hahn, Jenny Tung, Dietmar Zinner, Christian Roos, Clifford J. Jolly, Richard A. Gibbs, Kim C. Worley, Baboon Genome Analysis Consortium

^*Corresponding author for this work

Department of Molecular Biology and Genetics - Bioinformatics Research Centre (BiRC)

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Original language	English
Article number	6947
Journal	Science Advances
Volume	5
Issue	1
Number of pages	14
ISSN	2375-2548
DOIs	https://doi.org/10.1126/sciadv.aau6947
Publication status	Published - 30 Jan 2019

Keywords

ANUBIS
CONCORDANCE
EVOLUTIONARY
GENETICS
HAMADRYAS
HYBRID ZONE
HYBRIDIZATION PATTERNS
PHYLOGENY
PHYLOGEOGRAPHY
TREE

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Rogers, J., Raveendran, M., Alan Harris, R., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M., ... Baboon Genome Analysis Consortium (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1), Article 6947. https://doi.org/10.1126/sciadv.aau6947

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title = "The comparative genomics and complex population history of Papio baboons",

abstract = "Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.",

keywords = "ANUBIS, CONCORDANCE, EVOLUTIONARY, GENETICS, HAMADRYAS, HYBRID ZONE, HYBRIDIZATION PATTERNS, PHYLOGENY, PHYLOGEOGRAPHY, TREE",

author = "Jeffrey Rogers and Muthuswamy Raveendran and {Alan Harris}, R. and Thomas Mailund and Kalle Lepp{\"a}l{\"a} and Georgios Athanasiadis and Schierup, {Mikkel Heide} and Jade Cheng and Kasper Munch and Walker, {Jerilyn A.} and Konkel, {Miriam K.} and Vallmer Jordan and Steely, {Cody J.} and Beckstrom, {Thomas O.} and Christina Bergey and Andrew Burrell and Dominik Schrempf and Angela Noll and Maximillian Kothe and Kopp, {Gisela H.} and Yue Liu and Shwetha Murali and Konstantinos Billis and Martin, {Fergal J.} and Matthieu Muffato and Laura Cox and James Else and Todd Disotell and Muzny, {Donna M.} and Jane Phillips-Conroy and Bronwen Aken and Eichler, {Evan E.} and Tomas Marques-Bonet and Carolin Kosiol and Batzer, {Mark A.} and Hahn, {Matthew W.} and Jenny Tung and Dietmar Zinner and Christian Roos and Jolly, {Clifford J.} and Gibbs, {Richard A.} and Worley, {Kim C.} and {Baboon Genome Analysis Consortium}",

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Rogers, J, Raveendran, M, Alan Harris, R, Mailund, T, Leppälä, K, Athanasiadis, G, Schierup, MH , Cheng, J , Munch, K, Walker, JA, Konkel, MK, Jordan, V, Steely, CJ, Beckstrom, TO, Bergey, C, Burrell, A, Schrempf, D, Noll, A, Kothe, M, Kopp, GH, Liu, Y, Murali, S, Billis, K, Martin, FJ, Muffato, M, Cox, L, Else, J, Disotell, T, Muzny, DM, Phillips-Conroy, J, Aken, B, Eichler, EE, Marques-Bonet, T, Kosiol, C, Batzer, MA, Hahn, MW, Tung, J, Zinner, D, Roos, C, Jolly, CJ, Gibbs, RA, Worley, KC & Baboon Genome Analysis Consortium 2019, 'The comparative genomics and complex population history of Papio baboons', Science Advances, vol. 5, no. 1, 6947. https://doi.org/10.1126/sciadv.aau6947

TY - JOUR

T1 - The comparative genomics and complex population history of Papio baboons

AU - Rogers, Jeffrey

AU - Raveendran, Muthuswamy

AU - Alan Harris, R.

AU - Mailund, Thomas

AU - Leppälä, Kalle

AU - Athanasiadis, Georgios

AU - Schierup, Mikkel Heide

AU - Cheng, Jade

AU - Munch, Kasper

AU - Walker, Jerilyn A.

AU - Konkel, Miriam K.

AU - Jordan, Vallmer

AU - Steely, Cody J.

AU - Beckstrom, Thomas O.

AU - Bergey, Christina

AU - Burrell, Andrew

AU - Schrempf, Dominik

AU - Noll, Angela

AU - Kothe, Maximillian

AU - Kopp, Gisela H.

AU - Liu, Yue

AU - Murali, Shwetha

AU - Billis, Konstantinos

AU - Martin, Fergal J.

AU - Muffato, Matthieu

AU - Cox, Laura

AU - Else, James

AU - Disotell, Todd

AU - Muzny, Donna M.

AU - Phillips-Conroy, Jane

AU - Aken, Bronwen

AU - Eichler, Evan E.

AU - Marques-Bonet, Tomas

AU - Kosiol, Carolin

AU - Batzer, Mark A.

AU - Hahn, Matthew W.

AU - Tung, Jenny

AU - Zinner, Dietmar

AU - Roos, Christian

AU - Jolly, Clifford J.

AU - Gibbs, Richard A.

AU - Worley, Kim C.

AU - Baboon Genome Analysis Consortium

PY - 2019/1/30

Y1 - 2019/1/30

N2 - Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

AB - Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

KW - ANUBIS

KW - CONCORDANCE

KW - EVOLUTIONARY

KW - GENETICS

KW - HAMADRYAS

KW - HYBRID ZONE

KW - HYBRIDIZATION PATTERNS

KW - PHYLOGENY

KW - PHYLOGEOGRAPHY

KW - TREE

UR - http://www.scopus.com/inward/record.url?scp=85060670885&partnerID=8YFLogxK

U2 - 10.1126/sciadv.aau6947

DO - 10.1126/sciadv.aau6947

M3 - Journal article

C2 - 30854422

AN - SCOPUS:85060670885

SN - 2375-2548

VL - 5

JO - Science Advances

JF - Science Advances

IS - 1

M1 - 6947

ER -

The comparative genomics and complex population history of Papio baboons

Abstract

Keywords

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